Quantum chemical calculations on calcium oxalate and dolichin A and their binding efficacy to lactoferrin: An <i>in silico</i> study using DFT, molecular docking, and molecular dynamics simulations

Abstract

Lactoferrin, a member of the transferrin family, is one of the promoter proteins for calcium oxalate-type kidney stone formation. It exhibits a remarkable ability to interact with metals and oxalate ions. The prevalence of calcium oxalate in kidney stones was confirmed by the Fourier transform infrared spectra. The quantum chemical properties of calcium oxalate and dolichin A calculated by density functional theory and time-dependent density functional theory indicate their potential for hydrogen bonding and nonbonding interactions with the receptor proteins. From molecular docking analysis, the binding free energy of dolichin A was −7.78 kcal/mol, which was the best of twenty-four phytochemicals from Macrotyloma uniflorum, and that of calcium oxalate was −3.86 kcal/mol to lactoferrin. Furthermore, dolichin A having favorable physicochemical and pharmacokinetic properties offers post molecular dynamics molecular mechanics generalized Born surface area free energy of −17.61 ± 4.03 kcal/mol, indicating the strong binding interactions, and, therefore, it acts as a potential inhibitor of the lactoferrin.

Keywords

• kidney stones
• calcium oxalate and dolichin a
• lactoferrin
• density functional theory
• protein-ligand interaction